I love 999, I want to get Zero Escape but it is either that or Xenoblade on the New 3DS. I'm afraid it might also become rare, I know they are going to sell Xenoblade 3D in more places, but you can never be too sure. I will get Zero Escape at some point.
I've heard about the cover thing too, but the people who are complaining don't know how the Joker works. I never read the comics but I know that the Joker is really crazy and he does crazy things. I also know about the Killing Joke despite never reading it thanks to Cracked.com. All I can say is that there is no way DC (or Marvel) could get away releasing a comic/story like that without getting a huge amount of backlash from everyone.